SMTL ID : 5n3s.1

cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 4-Hydroxybenzamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

monomer

Ligands

1 x HBD: 4-HYDROXYBENZAMIDE(Non-covalent)

HBD.1: 13 residues within 4Å: Chain A: L.52, G.53, V.60, A.73, V.107, M.123, E.124, Y.125, V.126, E.130, L.176, T.186, F.330 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.60, A:V.60, A:A.73, A:L.176, A:F.330 Hydrogen bonds: A:E.124, A:V.126 Water bridges: A:L.52, A:E.130

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 6 residues within 4Å: Chain A: W.33, E.89, L.92, N.93, R.96, E.352 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.92 Hydrogen bonds: A:R.96, A:E.352 MPD.3: 11 residues within 4Å: Chain A: V.18, F.21, L.22, F.103, L.155, E.158, Y.159, K.295, W.305, I.306, Y.309 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:F.103, A:Y.309 Hydrogen bonds: A:E.158

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: Y.232, Y.238, R.259, F.260, P.261 No protein-ligand interaction detected (PLIP) DMS.5: 7 residues within 4Å: Chain A: L.201, C.202, G.203, T.204, P.205, L.208, Y.250 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oebbeke, M. et al., Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2018-02-28

Peptides

cAMP-dependent protein kinase catalytic subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cAMP-dependent protein kinase catalytic subunit alpha

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